This shows one of the many and very apparent faults of capturing HD video with a DSLR from Canon and other makes.
It happens because the camera does not bin the 18Mp down to a 2Mp (FullHD) when its capturing. It skips lines on the CMOS sensor instead, which is terrible in many ways, but given that these sensors aren't made for video its understandable.

This will "never" be fixed. All you can do is try no to film where there aren't apparent lines like this, or try to change angle somehow. Try also to set the sharpness on your current "Picture Style" all the way down.